tbuckley/cabot-search huggingface dataset:
Abstract 474: Integrating imaging and multi-omics data to elucidate racial differences in breast tumor biology to optimize precision oncology approaches and patient outcome
Authors: Nicole Liadis, Tyler Earnest, Eduardo Braun, Anu Antony, Lance Munn, Michael Hallock, Daniel Cook
Journal: Cancer Research (2022)

Abstract Background: Racial disparities in breast cancer incidence and clinical outcome have been well characterized. In particular, African American (AA) patients have higher mortality rates than other racial groups. Research into these racial disparities has primarily focused on socioeconomic determinants, with some studies exploring potential molecular determinants and limited biological differences found between AA and Caucasian patient tumors. Tumor intrinsic and extrinsic factors that promote racial differences in breast cancer development and patient outcome are not fully understood and strategies to address this are scarce. As a result, we have developed a platform that combines patient-specific imaging and multi-omics data to elucidate how biological differences integrate to promote racial disparities in tumor behavior and patient outcome. Methods: Imaging and transcriptomic data from over 500 patients were integrated within the SimBioSys TumoScope biophysical modeling software to understand racial differences in tumor biology and coordinated tumor behavior. Results: AA patients have tumors that display higher growth rates, characteristically have higher adipose tissue around the tumor, higher spatial variation in drug secretion, lower spatial variation in blood flow/and increased tumor stiffness. Conclusion: Using a transdisciplinary approach, our results show that metabolic and structural tumor features are associated with the disproportionately poor survival rates observed in AA breast cancer patients. By characterizing racial-specific tumor intrinsic and extrinsic biological factors and their potential interactions, strategies may emerge to personalize clinical management based on racial differences. In this way, precision oncology approaches can be applied to increase life-expectancy for racial minorities with breast cancer. Citation Format: Nicole Liadis, Tyler Earnest, Eduardo Braun, Anu Antony, Lance Munn, Michael Hallock, Daniel Cook, The SimBioSys Team. Integrating imaging and multi-omics data to elucidate racial differences in breast tumor biology to optimize precision oncology approaches and patient outcome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 474.
Abstract 1943: Elucidating early tumor microenvironmental changes due to immunotherapy with label-free Raman spectroscopy and machine learning
Authors: Santosh K. Paidi, Joel R. Troncoso, Narasimhan Rajaram, Ishan Barman
Journal: Cancer Research (2022)

Abstract Clinical benefit is observed in only a limited fraction of patients that undergo immunotherapy for a variety of cancer types. Therefore, the determination of robust biomarkers for accurate prediction of response to immunotherapeutic agents remains one of the grand challenges of 21st century. Our primary goal was to investigate if phenotypic differences due to treatment with ICI can be recognized with minimally perturbative molecular tools and guide personalization of immunotherapy. In this work, we provide first-in-class evidence that Raman spectroscopy (an optical method) and machine learning allows sensitive detection of early changes in biomolecular composition of tumors in response to immunotherapy with immune checkpoint inhibitors (ICI). By studying the widely investigated CT26 murine model of colorectal cancer treated with anti-CTLA-4 (n = 8) and anti-PD-L1 (n = 7) ICIs and controls (n = 10), we revealed new biological insights into the nature and degree of microenvironmental modifications induced by exposure to clinically relevant doses of ICI. Multivariate curve resolution-alternating least squares (MCR-ALS) decomposition of Raman spectral datasets revealed early changes in lipid, nucleic acid, and collagen content of the tumors following therapy. We trained supervised classification models - support vector machines and random forests on the spectral datasets and showed that the models provided excellent prediction accuracies for response to both ICIs and delineated spectral markers specific to each therapy, consistent with their differential mechanisms of action. On the basis of these findings, we sought to determine if the tumor microenvironment changes delineated by Raman spectroscopy correspond to proteomic alterations via quantitative mass spectrometry. Of the more than 6600 proteins identified, about 136 proteins were found to be significantly different in treated tumors relative to controls (p &amp;lt; 0.05 and log2 fold change of &amp;gt; 2). A subset of these differentially expressed proteins is known to regulate lipid metabolism and extracellular matrix composition, while others are known to control transcriptome dynamics or are associated with response to ICI therapy, thereby corroborating our Raman spectroscopic measurements. Our observation of biomolecular changes in the TME should catalyze detailed investigations for translating such markers and label-free Raman spectroscopy for clinical monitoring of immunotherapy response in cancer patients. Citation Format: Santosh K. Paidi, Joel R. Troncoso, Narasimhan Rajaram, Ishan Barman. Elucidating early tumor microenvironmental changes due to immunotherapy with label-free Raman spectroscopy and machine learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1943.
Abstract 5836: SMC4 promotes prostate cancer organ-specific metastasis by modifying cancer cell metabolism
Authors: Wei Zhang, Xin Huang, yueming Li, yingxuan Gong, xiuzhi Li
Journal: Cancer Research (2022)

Abstract Structural maintenance of chromosomes 4 (SMC4), one subunit of condensin complexes, is a key structural component of mitotic chromosomes. Accumulating evidence has suggested that SMC4 regulates prostate carcinogenesis. However, its roles on regulation of prostate cancer development remain unclear. Our previous studies showed that the expression of SMC4 is increased in highly lung-metastatic prostate cancer cells, RM1-LM, an organ-specific metastasis cell line that we developed. To investigate the function of SMC4, SMC4 gene was knockdown in RM1-LM cells by CRISPR/Cas9 system. Knockdown of SMC4 significantly diminished the cancer cell growth in RM1-LM. In addition, transwell assay results showed that SMC4 knockdown in RM1-LM suppressed the cell migration and invasion. Furthermore, we observed that SMC4 protein is important in the non-dividing phase of the cell cycle. In particular, cell cycle flow cytometry analysis indicated that SMC4 knockdown leaded to cell arrest in S phase. Finally, RM1-LM cells showed increased lung metastases compared with RM1-SMC4+/- cells in a murine model. The H&amp;E and IHC results confirmed that RM1-LM cells induced greater number of lung metastases and colonization than RM1-SMC4+/-cells, suggesting the loss of SMC4 suppressed prostate cancer metastasis. The interactome of SMC4 was uncovered through IP-MS and revealed that SMC4 may interacted with GLUT1, a key protein in glycolysis pathway. The ATP rate assay and Glycolysis rate assay illustrated a significantly metabolic switch existing in RM1-SMC4+/-cells compared with their parental cells. Collectively, our study suggested that the interaction between SMC4 and GLUT1, confirmed by Co-IP, promotes prostate cancer cells metastasis via modifying the cell metabolism. This work was supported by NSFC projects 81802949, 81773146, 81972766, 81972420, 82173336; Shenzhen Science and Technology Commission Project JCYJ20190809161811237, JCYJ2021032410424040; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research (2017B030301018);and College students' innovative entrepreneurial training program (S202114325028) Citation Format: Wei Zhang, Xin Huang, yueming Li, yingxuan Gong, xiuzhi Li. SMC4 promotes prostate cancer organ-specific metastasis by modifying cancer cell metabolism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5836.
Abstract 3209: Everolimus inhibits angiogenesis and lymphangiogenesis to affect tumor growth in <i>TP53</i> mutant HNSCC
Authors: Md Maksudul Alam, Janmaris Marin Fermin, Mark Knackstedt, Mackenzie J. Noonan, Emily K. Daniel, Tara Moore-Medlin, Xiaohua Rong, Alok R. Khandelwal, Cherie-Ann O. Nathan
Journal: Cancer Research (2022)

Abstract Head and neck squamous cell carcinoma (HNSCC) constitutes the eighth most common cancer globally, with the eighth highest mortality rate amongst all cancer types. TP53 is the most frequently mutated gene in HPV -negative HNSCC. HPV-negative HNSCC harboring p53 mutations have the worst clinical outcomes with 50-60% local regional and distant recurrences causing increased morbidity and mortality. TP53 mutations are associated with shorter recurrence-free and overall survival. Angiogenesis and lymphangiogenesis play a causal role in tumor recurrence and lymph node metastasis. Therefore, inhibiting tumor angiogenesis and lymphangiogenesis is important in to preventing tumor recurrence and metastasis of TP53 mutant HNSCC. Previous studies demonstrated that mTOR activates STAT3 to upregulate HIF-1α and its target proteins, VEGF-A and VEGF-C, key molecules involved in angiogenesis and lymphangiogenesis, respectively. Further, mTOR inhibitors suppress autocrine and paracrine growth stimulation of tumor and lymphatic endothelial cells by impairing the VEGF-C/VEGF-3 axis and releasing soluble VEGFR-2. Accordingly, our objective was to investigate the effect of an mTOR inhibitor, everolimus, on angiogenesis and lymphangiogenesis of HPV-negative TP53 mutant HNSCC. Everolimus treatment of HPV-negative HNSCC cell lines harboring a variety of TP53 mutations, significantly downregulated protein and mRNA levels of VEGF-A and VEGF-C. Moreover, everolimus downregulated HIF-1α protein levels suggesting a HIF-1alpha-dependent VEGF modulation. Interestingly, treatment of human microvascular and lymphatic endothelial cells (HMEC-1 and HMEC-1A, respectively) with everolimus was also associated with a significant reduction in cell proliferation, in vitro tube formation, and migration. Protein and mRNA levels of HIF-1α, VEGF-A, and VEGF-C were downregulated by everolimus treatment in both HMEC-1 and HMEC-1A cell lines. Taken together, our data suggest that everolimus prevents angiogenesis and lymphangiogenesis through the inhibition of HIF-1α, indicating a promising role for mTOR inhibitors in treating HPV-negative TP53 mutant HNSCC patients at high risk for recurrence. Citation Format: Md Maksudul Alam, Janmaris Marin Fermin, Mark Knackstedt, Mackenzie J. Noonan, Emily K. Daniel, Tara Moore-Medlin, Xiaohua Rong, Alok R. Khandelwal, Cherie-Ann O. Nathan. Everolimus inhibits angiogenesis and lymphangiogenesis to affect tumor growth in TP53 mutant HNSCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3209.
Abstract 1623: AXL-STAT3 targeting of lung tumor microenvironments
Authors: Josephine Amalia Taverna, Chia-Nung Hung, Meizhen Chen, Joel Michalek, Chun-Liang Chen, Nameer Kirma, Chih-Wei Chou, Xi Tan, Chiou-Miin Wang, Zhang Zhao, Duy Nguyen, Daniel DeArmond, Tim Huang
Journal: Cancer Research (2022)

Abstract Dynamic tumor microenvironments contain a myriad of cell subtypes, each providing a unique functionality in support of malignant growth. To prepare a metastatic niche, a tight network must be present to coordinate the delivery and sharing of co-stimulatory signals among malignant tumor epithelial cells and supportive host cells. AXL and STAT3 cascades are critical components of intracellular signaling networks, as they translate multiple external stimuli into specific cellular responses. Single cell profiling of lung tumors reveals that AXL collaborates with STAT3 to create a unified tumor ecosystem favoring hybrid epithelial-to-mesenchymal transition states of lung epithelial cells, pro-tumorigenic remodeling of fibroblasts and M2 polarization of macrophages. Disruption of AXL-STAT3 circuit with AXL inhibitor and JAK inhibitor not only compromises this co-dependency in A549 lung cancer cells implanted in xenograft mice, but also limits their ability to conscript murine fibroblasts, macrophages and other immune cells that form a symbiotic community for tumor growth. Our preclinical work suggests that combined targeting of AXL-STAT3 circuit could disturb the communication among diverse cell subtypes in the lung tumor microenvironment, thus limiting the metastatic progression. Our co-culture studies reveal that AXL signaling in lung cancer cells and fibroblasts exerts an IL-11 mediated paracrine effect on macrophages to sustain STAT3 signaling for M2 polarization and cancer stemness mimicry. In vivo drug testing in A549 mouse xenograft model demonstrate that AXL-STAT3 inhibition leads to reduction in host cell recruitment and attenuates M2 polarization of macrophages and pro-tumorigenic remodeling of stromal fibroblasts. AXL-STAT3 targeting to dismantle lung tumor microenvironments is a promising therapeutic strategy and may establish new treatment paradigms for patients with lung adenocarcinoma. Citation Format: Josephine Amalia Taverna, Chia-Nung Hung, Meizhen Chen, Joel Michalek, Chun-Liang Chen, Nameer Kirma, Chih-Wei Chou, Xi Tan, Chiou-Miin Wang, Zhang Zhao, Duy Nguyen, Daniel DeArmond, Tim Huang. AXL-STAT3 targeting of lung tumor microenvironments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1623.
MERTK activation drives osimertinib resistance in EGFR-mutant non–small cell lung cancer
Authors: Dan Yan, Justus M. Huelse, Dmitri Kireev, Zikang Tan, Luxiao Chen, Subir Goyal, Xiaodong Wang, Stephen V. Frye, Madhusmita Behera, Frank Schneider, Suresh S. Ramalingam, Taofeek Owonikoko, H. Shelton Earp, Deborah DeRyckere, Douglas K. Graham
Journal: Journal of Clinical Investigation (2022)

Acquired resistance is inevitable in non–small cell lung cancers (NSCLCs) treated with osimertinib (OSI), and the mechanisms are not well defined. The MERTK ligand GAS6 promoted downstream oncogenic signaling in EGFR-mutated (EGFRMT) NSCLC cells treated with OSI, suggesting a role for MERTK activation in OSI resistance. Indeed, treatment with MRX-2843, a first-in-class MERTK kinase inhibitor, resensitized GAS6-treated NSCLC cells to OSI. Both GAS6 and EGF stimulated downstream PI3K/AKT and MAPK/ERK signaling in parental cells, but only GAS6 activated these pathways in OSI-resistant (OSIR) derivative cell lines. Functionally, OSIR cells were more sensitive to MRX-2843 than parental cells, suggesting acquired dependence on MERTK signaling. Furthermore, MERTK and/or its ligands were dramatically upregulated in EGFRMT tumors after treatment with OSI in both xenograft models and patient samples, consistent with induction of autocrine/paracrine MERTK activation. Moreover, treatment with MRX-2843 in combination with OSI, but not OSI alone, provided durable suppression of tumor growth in vivo, even after treatment was stopped. These data identify MERTK as a driver of bypass signaling in treatment-naive and EGFRMT-OSIR NSCLC cells and predict that MRX-2843 and OSI combination therapy will provide clinical benefit in patients with EGFRMT NSCLC.
Abstract 6007: Identification of drivers of soft tissue sarcoma metastasis
Authors: Janai R. Carr-Ascher, Maria Munoz
Journal: Cancer Research (2022)

Abstract Soft tissue sarcomas are a rare and heterogeneous group of tumors with a 65% five-year survival rate despite aggressive treatment with surgery, radiation, and chemotherapy. Even with intensive multimodality treatment, many patients will develop incurable metastatic disease, providing evidence that our current therapies are ineffective and new treatments are desperately needed. Pre-clinical models to study metastasis of human soft tissue sarcomas are limited. We have developed a system that allows for the formation of distinct soft tissue sarcoma subtypes from mesenchymal stem cells that have been depleted of p53 and Rb1 using CRISPR. Injection of these cells intramuscularly results in metastasis to the lung. Using this novel model system, we have performed a genetic screen to identify pathways and specific drivers of sarcoma metastasis. This pre-clinical in vivo model system will allow for the identification of putative therapeutic targets to prevent the development of lethal metastatic growth. Citation Format: Janai R. Carr-Ascher, Maria Munoz. Identification of drivers of soft tissue sarcoma metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6007.
Enzalutamide Monotherapy vs Active Surveillance in Patients With Low-risk or Intermediate-risk Localized Prostate Cancer
Authors: Neal D. Shore, Joseph Renzulli, Neil E. Fleshner, Courtney M. P. Hollowell, Srinivas Vourganti, Jonathan Silberstein, Rizwan Siddiqui, John Hairston, Dina Elsouda, David Russell, Matthew R. Cooperberg, Scott A. Tomlins
Journal: JAMA Oncology (2022)

There are few published studies prospectively assessing pharmacological interventions that may delay prostate cancer progression in patients undergoing active surveillance (AS).
Abstract 6298: The novel long noncoding RNA lncNeur promotes neuroblastoma by up-regulating AURKA and Myc expression
Authors: Jing Wu, Pei Yan Liu, Belamy Cheung, Glenn Marshall, Marcel Dinger, Tao Liu
Journal: Cancer Research (2022)

Abstract Background: Neuroblastoma is the most common solid tumor in early childhood, and accounts for approximately 15% of childhood cancer death. We have recently analyzed RNA sequencing data from 493 human neuroblastoma tissues, and identified the long noncoding RNA lincNeur as one of the transcripts, high expression of which most considerably correlated with poor prognosis in both MYCN oncogene-amplified and MYCN non-amplified neuroblastoma patients. Aims: To determine the tumorigenic role of lincNeur in neuroblastoma, and to identify the mechanism of action through which lincNeur exerts oncogenic function, also to screen for small molecule compound inhibitors of lincNeur. Methods and results: We performed RNA-binding protein pull-down assay and RNA-immunoprecipitation assay. RALY was identified and validated as one of the binding proteins of lincNeur. We also identified down-stream targets of lincNeur via genome-wide differential gene expression analysis. E2F1 and AURKA were identified as among the transcripts significantly down-regulated after lincNeur knockdown. RT-PCR and western blot analysis showed that lincNeur knockdown reduced E2F1 and AURKA mRNA and protein expression, and reduced N-Myc and c-Myc protein but not mRNA expression. In addition, lincNeur or RALY knockdown reduced, while over-expression of lincNeur or RALY promoted, neuroblastoma cell proliferation. We also demonstrated lincNeur knockdown significantly suppressed RALY protein binding to E2F1 and AURKA mRNAs. Mouse xenograft model experiment showed that lincNeur knockdown suppressed neuroblastoma tumor progression in vivo. Importantly, we have confirmed the binding site between lincNeur and RALY, and are screening small molecule compound libraries for inhibitors of lincNeur and RALY interaction for neuroblastoma therapy. Conclusions: The novel long noncoding RNA lincNeur promotes neuroblastoma by interacting with RALY to up-regulate E2F1 and AURKA mRNA and protein, as well as N-Myc and c-Myc protein expression. Small molecule compound inhibitors of lincNeur and RALY interaction is a promising therapeutic approach. Citation Format: Jing Wu, Pei Yan Liu, Belamy Cheung, Glenn Marshall, Marcel Dinger, Tao Liu. The novel long noncoding RNA lncNeur promotes neuroblastoma by up-regulating AURKA and Myc expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6298.
Abstract 643: Non-classical sources of tumour specific antigen in checkpoint inhibitor response
Authors: Krupa Thakkar, Danwen Qian, Hongui Cha, Thomas B. Watkins, Charles Swanton, Kevin Litchfield
Journal: Cancer Research (2022)

Abstract A large-scale meta-analysis of over 1000 CPI (immune checkpoint blockade) treated patients across multiple cancer types broadly categorised biomarkers into four categories: sources of antigen leading to T-cell responses, host-derived factors, immune evasion and infiltration mechanisms. Our analyses established tumour mutation burden (TMB) as the strongest predictor of CPI response, alongside clonal TMB and CXCL9 expression. However, over half of the patients in our cohort who responded to CPI treatment did not have high-TMB and showed no evidence of oncogenic viral infections, hence suggesting alternative sources of antigen could be driving the immune response. As well as this, data from the CPI1000 cohort suggested that the biomarkers identified in an extensive systematic review only accounted for ~60% of the variance in CPI response, promoting the search for non-classical sources of antigen. Extending the cohort to encompass 2500+ patients, using available genomic and transcriptomic data from checkpoint inhibitor trials and industry partners, the previously published multivariate predictor will be further validated in a larger patient cohort inclusive of more cancer types. The CPI1000 cohort utilised primarily whole exome-sequencing therefore, had limited ability to discern non-coding sources of tumour antigen and cell-type specific predictors of response. The CPI2500+ cohort will incorporate several additional cohorts as well as single-cell and T-cell reactivity data. The raw data will be harmonised across studies and processed using a robust bioinformatics pipeline. As well as this, alternative (non-classical) sources of tumour specific antigen will be studied. Alternative sources of antigen can originate from a diverse range of biological processes including retained introns, stop codon loss mutations and cancer associated bacterial/viral epitopes. Data from this exploratory analysis will be coupled with peptide reactivity assays from local UCL patient TIL (tumour infiltrating lymphocyte) and PMBC (peripheral blood mononuclear cells) samples to validate immunogenicity. Current analysis has identified a novel subgroup of CPI-responders with low-TMB who have significantly higher rates of microbial diversity, consistent with a diverse tumour microbiome providing a source of immunogenic antigens in the absence of high-TMB. Here we will present insights from CPI2500+ and highlight the importance of emerging non-classical sources of tumour specific antigen. Citation Format: Krupa Thakkar, Danwen Qian, Hongui Cha, Thomas B. Watkins, Charles Swanton, Kevin Litchfield. Non-classical sources of tumour specific antigen in checkpoint inhibitor response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 643.